Normally, when combining recorded audio tracks with MIDI tracks, you would record the MIDI tracks first, giving yourself a solid reference and sync source when recording the subsequent audio tracks.
But, you may occasionally run into situations where you will be recording audio tracks to tape or disk before completing the MIDI tracks. If you find yourself in this situation, it is a good idea to record all of your audio tracks referenced to a MIDI click, generated by locking your sequencer to timecode. Then when you start recording your MIDI tracks, it will be a simple task to sync back with the pre-recorded audio tracks. Assuming the audio is recorded fairly tightly with the MIDI click, it will still be possible to edit and quantize your MIDI tracks without losing sync between the recorded and sequenced tracks.